[headers, positions, copyNumbers] = readData('T16.100cells.cn.txt');
numCells = length(copyNumbers(:,1));
numSites = length(copyNumbers);
distMatrix = ones(numCells);

for i=1:numCells
    for j=1:numCells
		for window = 3
			distMatrix(i,j)=getTransitionProfileDistances(i,j,copyNumbers, window);
		end
    end
end

tree = seqneighjoin(distMatrix,'equivar',headers);
plot(tree,'Orientation','top')